1. Field of the Invention
The present invention relates to novel polynucleotides derived from microorganisms belonging to coryneform bacteria and fragments thereof, polypeptides encoded by the polynucleotides and fragments thereof, polynucleotide arrays comprising the polynucleotides and fragments thereof, computer readable recording media in which the nucteotide sequences of the polynucleotide and fragments thereof have been recorded, and use of them as well as a method of using the polynucleotide and/or polypeptide sequence information to make comparisons.
2. Brief Description of the Background Art
Coryneform bacteria are used in producing various useful substances, such as amino acids, nucleic acids, vitamins, saccharides (for example, ribulose), organic acids (for example, pyruvic acid), and analogues of the above-described substances (for example, N-acetylamino acids) and are very useful microorganisms industrially. Many mutants thereof are known.
For example, Corynebacterium glutamicum is a Gram-positive bacterium identified as a glutamic acid-producing bacterium, and many amino acids are produced by mutants thereof. For example, 1,000,000 ton/year of L-glutamic acid which is useful as a seasoning for umami (delicious taste), 250,000 ton/year of L-lysine which is a valuable additive for livestock feeds and the like, and several hundred ton/year or more of other amino acids, such as L-arginine, L-proline, L-glutamine, L-tryptophan, and the like, have been produced in the world (Nikkei Bio Yearbook 99, published by Nikkei BP (1998)).
The production of amino acids by Corynebacterium glutamicum is mainly carried out by its mutants (metabolic mutants) which have a mutated metabolic pathway and regulatory systems. In general, an organism is provided with various metabolic regulatory systems so as not to produce more amino acids than it needs. In the biosynthesis of L-lysine, for example, a microorganism belonging to the genus Corynebacterium is under such regulation as preventing the excessive production by concerted inhibition by lysine and threonine against the activity of a biosynthesis enzyme common to lysine, threonine and methionine, i.e., an aspartokinase, (J. Biochem., 65: 849-859 (1969)). The biosynthesis of arginine is controlled by, repressing the expression of its biosynthesis gene by arginine so as not to biosynthesize an excessive amount of arginine (Microbiology, 142: 99-108 (1996)). It is considered that these metabolic regulatory mechanisms are deregulated in amino acid-producing mutants. Similarly, the metabolic regulation is deregulated in mutants producing nucleic acids, vitamins, saccharides, organic acids and analogues of the above-described substances so as to improve the productivity of the objective product.
However, accumulation of basic genetic, biochemical and molecular biological data on coryneform bacteria is insufficient in comparison with Escherichia coli, Bacillus subtilis, and the like. Also, few findings have been obtained on mutated genes in amino acid-producing mutants. Thus, there are various mechanisms, which are still unknown, of regulating the growth and metabolism of these microorganisms.
A chromosomal physical map of Corynebacterium glutamicum ATCC 13032 is reported and it is known that its genome size is about 3,100 kb (Mol. Gen. Genet., 252: 255-265 (1996)). Calculating on the basis of the usual gene density of bacteria, it is presumed that about 3,000 genes are present in this genome of about 3,100 kb. However, only about 100 genes mainly concerning amino acid biosynthesis genes are known in Corynebacterium glutamicum, and the nucleotide sequences of most genes have not been clarified hitherto.
In recent years, the full nucleotide sequence of the genomes of several microorganisms, such as Escherichia coli, Mycobacterium tuberculosis, yeast, and the like, have been determined (Science, 277: 1453-62 (1997); Nature, 393: 537-544 (1998); Nature, 387: 5-105 (1997)). Based on the thus determined full nucleotide sequences, assumption of gene regions and prediction of their function by comparison with the nucleotide sequences of known genes have been carried out. Thus, the functions of a great number of genes have been presumed, without genetic, biochemical or molecular biological experiments.
In recent years, moreover, techniques for monitoring expression levels of a great number of genes simultaneously or detecting mutations, using DNA chips, DNA arrays or the like in which a partial nucleic acid fragment of a gene or a partial nucleic acid fragment in genomic DNA other than a gene is fixed to a solid support, have been developed. The techniques contribute to the analysis of microorganisms, such as yeasts, Mycobacterium tuberculosis, Mycobacterium bovis used in BCG vaccines, and the like (Science, 278: 680-686 (1997); Proc. Natl. Acad. Sci. USA, 96: 12833-38 (1999); Science, 284: 1520-23 (1999)).